Hello,
I have been trying to get daa-meganizer to work using MEGAN6 in a cluster. I have tried:
daa-meganizer -i 13_raw_contigs.da -mdb megan-map-Feb2022.zip
/vast/megan/tools/daa-meganizer -i 13_raw_contigs.da -mdb megan-map-Feb2022.zip
Neither code has worked, and I always receive the “No such file or directory” message after running them. Is my code incorrect?
Thank you for your help
Hi @lyisrae1,
Is the file 13_raw_contigs.da present in the folder? Please check it. Also, note that the DIAMOND-generated DAA file should be 13_raw_contigs.daa, but it seems you’re missing one a.
Anupam
Hello Anupam,
Thank you for the catch. I was able to figure out what was wrong soon after I posted by talking to my university’s cluster’s IT personnel.
However, I do have another question about using DIAMOND+MEGAN for aligning my contigs with DNA databases. I have been able to find a manual for aligning to nr in NCBI, but there are not instructions for building an index using DNA databases with Diamond. May I have some instruction or info on that please?
Hi @lyisrae1,
DIAMOND only supports nucleotide-to-protein alignment (blastx, translated) or protein-to-protein alignment (blastp). For nucleotide-to-nucleotide alignment, you may need to use other tools like blastn or LAST. We also have MALT, but that’s typically used for aligning ancient DNA reads.
Given that contigs are long, you can treat them like long reads. Check if the aligner you’re using has any specific flags for handling this. I believe researchers often use LAST for alignment in such cases, and the subsequent processing with MEGAN remains the same.
Best regards,
Anupam
Hello Anupam,
Thank you for the tip. I tried to look through some old links to download the MALT maps and database, but it brings me to a 404 error page. Can you give me the correct link please?
Thanks,
Leone